This paper investigates the structural and magnetic properties of hexagonal Ba(Ti 1−x Fe x )O 3−δ (x=0.3 and 0.7) ceramics, synthesized with solid-state reaction method. Transmission electron microscope investigations reveal that structural phase separation featured by non-modulated and modulated phases is identified by the electron diffraction patterns taken along [001] zone axis in x=0.3 sample (BTF30). While for x=0.7 sample (BTF70), a pure phase with commensurate and incommensurate modulations at different directions is identified. The superstructure peaks observed in their X-ray diffraction patterns are verified by their individual commensurate modulation, q s =1/2 (31-2) in the modulated phase of BTF30 and q 4 , −1 =4/9(304)–(001) in BTF70. In addition to the room-temperature weak ferromagnetism of BTF30 and paramagnetism of BTF70, spin glass transitions with T f =3.4K for the former and T f =33.6K for the latter are observed. On the basis of the structural characteristics, the influence of O1 and O2 vacancies on magnetic and dielectric properties of the doped system is discussed.